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Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 BuviA.00061.c.B1.PS02389 at 24.8 mg/ml incubated with 3 mM UDP-N-acetylglucosamine, then then mixed 1:1 with MCSG1(f5): 20% PEG-3350, 0.2 M sodium acetate, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.78 55.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116 α = 90 b = 81.41 β = 98.03 c = 55.16 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD Beryllium Lenses 2015-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 50 97 0.049 0.056 18.04 4.1 87041 -3 12.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.49 94.3 0.527 0.626 2.22 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1vgv 1.45 27.31 83489 4134 93.03 0.1357 0.1344 0.135 0.159 0.1583 19.7916
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.598 f_angle_d 1.133 f_chiral_restr 0.068 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 87
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction BALBES phasing